Climate change in the Arctic leads to permafrost degradation and to associated changes infreshwater geochemistry. There is a limited understanding of how disturbances such as active layerdetachments or retrogressive thaw slumps impact water quality on a catchment scale. This study investigateshow permafrost degradation affects concentrations of dissolved organic carbon (DOC), total dissolvedsolids (TDS), suspended sediment, and stable water isotopes in adjacent Low Arctic watersheds. Weincorporated data on disturbance between 1952 and 2015, as well as sporadic runoff and geochemistry dataof streams nearby. Our results show that the total disturbed area decreased by 41% between 1952 and 2015,whereas the total number of disturbances increased by 66% in all six catchments. The spatial variabilityof hydrochemical parameters is linked to catchment properties and not necessarily reflected at the outflow.Degrading ice‐wedge polygons were found to increase DOC concentrations upstream in Ice Creek West,whereas hydrologically connected disturbances were linked to increases in TDS and suspended sediment.Although we found a great spatial variability of hydrochemical concentrations along the paired watershed,there was a linear relationship between catchment size and daily DOC, total dissolved nitrogen, and TDSfluxes for all six streams. Suspended sedimentflux on the contrary did not show a clear relationship as onehydrologically connected retrogressive thaw slump impacted the overallflux in one of the streams.Understanding the spatial variability of water quality will help to model the lateral geochemicalfluxes fromArctic catchments